getSeqsAcrossBSJs: Retrieve back-spliced junction sequences

In circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Description

The function getSeqsAcrossBSJs() retrieves the sequences across the back-spliced junctions. A total of 11 nucleotides from each side of the back-spliced junction are taken and concatenated together.

Usage

getSeqsAcrossBSJs(annotatedBSJs, gtf, genome)

Arguments

annotatedBSJs	A data frame with the annotated back-spliced junctions. It can be generated with annotateBSJs.
gtf	A dataframe containing genome annotation information. It can be generated with formatGTF.
genome	A BSgenome object containing the genome sequences. It can be generated with getBSgenome. See available.genomes to see the BSgenome package currently available.

Value

A list.

Examples

# Load a data frame containing detected back-spliced junctions
data("mergedBSJunctions")

# Load short version of the gencode v19 annotation file
data("gtf")

# Annotate the first back-spliced junctions
annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

# Get genome
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)){

genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

# Retrieve target sequences
targets <- getSeqsAcrossBSJs(
    annotatedBSJs,
    gtf,
    genome)
}

circRNAprofiler documentation built on March 6, 2021, 2 a.m.